Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_068170828.1 HTA01S_RS10535 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_001592305.1:WP_068170828.1 Length = 503 Score = 152 bits (383), Expect = 3e-41 Identities = 111/343 (32%), Positives = 176/343 (51%), Gaps = 18/343 (5%) Query: 69 PAALQYAASEGYAPLRQAIADFL----PWDVDADQILITTGSQQALDLIAKVLIDENSRV 124 P L Y S GYAPLR+AIAD+L +DADQ+++TTG+QQ+L+L A++L D V Sbjct: 163 PDMLDYNDSGGYAPLRRAIADYLRVFRSVQLDADQVIVTTGTQQSLELCARLLADHGDTV 222 Query: 125 LVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPT 184 VE P Y GA++AF ++ V DDEG+ A + +Y+ P+ Q PT Sbjct: 223 WVEDPAYWGAVKAFMATGLAIHPVPVDDEGI-----HPGTADDAHPPKLIYLTPSHQYPT 277 Query: 185 GRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCI-YMGSFSKV 243 G M+ RR L+ A ++ED+ + F PP + L + +G + YMG+FSKV Sbjct: 278 GAVMSLPRRHQLLSTARAHGAWVLEDDYDSEYRFSGPPISSLEGLDNDGRVFYMGTFSKV 337 Query: 244 LAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYN--QRLVAEVMKGNFLDRHVPTIRAL 301 L PG++LG+++AP+ + QA DL+ PG Q +AE ++ + R Sbjct: 338 LYPGIKLGYLIAPRPLAAAFKQAHY--DLNRPGQMPLQAALAEFIEMGHFSSALRRARQN 395 Query: 302 YKQQCEAMLAALTQEMAGLGVEW---NRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFV 358 Y ++ A+L AL +A G E + + G+ L +RLP + L + ++ + Sbjct: 396 YGERRAALLDALKPVLAP-GTEGPFISGAEQGLHLCLRLPATVDDAALAQRIAQQGLTVR 454 Query: 359 PGAAFYADNADPRTLRLSFVTSTVEQIATGIAALAAAIRSHKG 401 P +A+ D + L + + + + +I LAAA+R G Sbjct: 455 PLSAYCLARHDLKGLVIGYGYAPLREIQRCGPVLAAAVRQALG 497 Lambda K H 0.318 0.134 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 482 Number of extensions: 33 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 401 Length of database: 503 Length adjustment: 33 Effective length of query: 368 Effective length of database: 470 Effective search space: 172960 Effective search space used: 172960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory